TGCA数据挖掘1---R包安装
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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> options("repos" = c(CRAN="mirrors.tuna.tsinghua.edu/CRAN/"))
> if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
载⼊需要的程辑包：BiocManager
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
>
> options(BioC_mirror="mirrors.tuna.tsinghua.edu/bioconductor/")
>
> cran_packages <- c('tidyr',
+ 'tibble',
+ 'dplyr',
+ 'stringr',
+ 'ggplot2',
+ 'ggpubr',
+ 'factoextra',
+ 'FactoMineR',
+ 'pheatmap',
+ "survival",
+ "survminer",
+ "patchwork",
+ "ggstatsplot",
+ "ggplotify",
+ "cowplot",
+ "glmnet",
+ "ROCR",
+ "caret",
+ "randomForest",
+ "survminer",
+ "Hmisc",
+ "e1071",
+ "deconstructSigs",
+ "timeROC"
+ )
> Biocductor_packages <- c("KEGG.db",
+ "limma",
+ "clusterProfiler",
+ "db",
+ "SummarizedExperiment",
+ "DESeq2",
+ "edgeR",
+ "ggpubr",
+ "rtracklayer",
+ "genefilter",
+ "maftools",
+ "ComplexHeatmap",
+ "GDCRNATools"
+ )
>
>
恶搞电影> for (pkg in cran_packages){
+ if (! require(ly=T) ) {
+ install.packages(pkg,ask = F,update = F)
+ require(ly=T)
景色英文+ }
+ }
载⼊需要的程辑包：tidyr
载⼊需要的程辑包：tibble
载⼊需要的程辑包：dplyr
载⼊程辑包：‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:ba’:
interct, tdiff, tequal, union
载⼊需要的程辑包：stringr
载⼊需要的程辑包：ggplot2
U suppressPackageStartupMessages() to eliminate package startup messages
载⼊需要的程辑包：ggpubr
载⼊需要的程辑包：factoextra
Welcome! Want to learn more? See two factoextra-related books at goo.gl/ve3WBa 载⼊需要的程辑包：FactoMineR
载⼊需要的程辑包：pheatmap
载⼊需要的程辑包：survival
载⼊需要的程辑包：survminer
载⼊需要的程辑包：patchwork
载⼊需要的程辑包：ggstatsplot
Registered S3 methods overwritten by 'lme4':
method from
cooks.Mod car
Mod car
Mod car
In ca you would like cite this package, cite it as:
Patil, I. (2018). ggstatsplot: "ggplot2" Bad Plots with Statistical Details. CRAN.
Retrieved from cran.r-project/web/packages/ggstatsplot/index.html
载⼊需要的程辑包：ggplotify
载⼊需要的程辑包：cowplot
载⼊程辑包：‘cowplot’
The following object is masked from ‘package:patchwork’:
align_plots
The following object is masked from ‘package:ggpubr’:
get_legend
载⼊需要的程辑包：glmnet
载⼊需要的程辑包：Matrix
载⼊程辑包：‘Matrix’
The following objects are masked from ‘package:tidyr’:
expand, pack, unpack
Loaded glmnet 4.1
载⼊需要的程辑包：ROCR
载⼊需要的程辑包：caret
载⼊需要的程辑包：lattice
载⼊程辑包：‘caret’
The following object is masked from ‘package:survival’:
cluster
cluster
载⼊需要的程辑包：randomForest
randomForest 4.6-14
Type rfNews() to e new features/changes/bug fixes.
载⼊程辑包：‘randomForest’
msn广告
The following object is masked from ‘package:ggplot2’:
margin
The following object is masked from ‘package:dplyr’:
combine
载⼊需要的程辑包：Hmisc
载⼊需要的程辑包：Formula
载⼊程辑包：‘Hmisc’
The following objects are masked from ‘package:dplyr’:
src, summarize
The following objects are masked from ‘package:ba’:
format.pval, units
载⼊需要的程辑包：e1071
载⼊程辑包：‘e1071’
The following object is masked from ‘package:Hmisc’:
impute
载⼊需要的程辑包：deconstructSigs
载⼊需要的程辑包：timeROC
>
>
> # u BiocManager to install
> for (pkg in Biocductor_packages){
+ if (! require(ly=T) ) {
+ BiocManager::install(pkg,ask = F,update = F)
+ require(ly=T)
+ }
+ }
载⼊需要的程辑包：KEGG.db
载⼊需要的程辑包：AnnotationDbi
载⼊需要的程辑包：stats4
关于中秋节的图片载⼊需要的程辑包：BiocGenerics
载⼊需要的程辑包：parallel
载⼊程辑包：‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:randomForest’:
combine
The following objects are masked from ‘package:dplyr’:
combine, interct, tdiff, union
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:ba’:
anyDuplicated, append, as.data.frame, baname, cbind, colnames, dirname,
do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, interct,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, tdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
载⼊需要的程辑包：Bioba
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browVignettes()'. To cite
Bioconductor, e 'citation("Bioba")', and for packages
'citation("pkgname")'.
载⼊程辑包：‘Bioba’
The following object is masked from ‘package:Hmisc’:
contents
载⼊需要的程辑包：IRanges
载⼊需要的程辑包：S4Vectors
载⼊程辑包：‘S4Vectors’
The following object is masked from ‘package:Matrix’:
expand
The following objects are masked from ‘package:dplyr’:
first, rename子路
The following object is masked from ‘package:tidyr’:
expand
The following object is masked from ‘package:ba’:
载⼊程辑包：‘IRanges’
The following objects are masked from ‘package:dplyr’:
collap, desc, slice
The following object is masked from ‘package:grDevices’:
windows
载⼊程辑包：‘AnnotationDbi’
The following object is masked from ‘package:dplyr’:
lect
KEGG.db contains mappings bad on older data becau the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions of
Bioconductor may not have it available. Urs who want more current data are
encouraged to look at the KEGGREST or reactome.db packages
载⼊需要的程辑包：limma
载⼊程辑包：‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
载⼊需要的程辑包：clusterProfiler
clusterProfiler v3.18.0 For help: guangchuangyu.github.io/software/clusterProfiler
If you u clusterProfiler in published rearch, plea cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integra 载⼊程辑包：‘clusterProfiler’
The following object is masked from ‘package:AnnotationDbi’:
lect
The following object is masked from ‘package:IRanges’:
slice
The following object is masked from ‘package:S4Vectors’:
rename
系统启动项The following object is masked from ‘package:lattice’:
dotplot
The following object is masked from ‘package:stats’:
filter
载⼊需要的程辑包：db
载⼊需要的程辑包：SummarizedExperiment
载⼊需要的程辑包：MatrixGenerics
载⼊需要的程辑包：matrixStats
载⼊程辑包：‘matrixStats’
The following objects are masked from ‘package:Bioba’:
anyMissing, rowMedians
The following object is masked from ‘package:dplyr’:
count
载⼊程辑包：‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollap, colCounts,
colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs,
colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians,
colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks,
colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars,
colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollap,
rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2,
rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges,
rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds,
rowWeightedVars
The following object is masked from ‘package:Bioba’:
rowMedians培训小游戏
载⼊需要的程辑包：GenomicRanges
